A Predictive Model for Transcriptional Control of Physiology in a Free Living Cell

Richard Bonneau, Marc T. Facciotti, David J. Reiss, Amy K. Schmid, Min Pan, Amardeep Kaur, Vesteinn Thorsson, Paul Shannon, Michael Johnson, J. Christopher Bare, William Longabaugh, Madhavi Vuthoori, Kenia Whitehead, Aviv Madar, Lena Suzuki, Tetsuya Mori, Dong Eun Chang, Jocelyne DiRuggiero, Carl H. Johnson, Leroy Hood & 1 others Nitin S. Baliga

Research output: Contribution to journalArticle

Abstract

The environment significantly influences the dynamic expression and assembly of all components encoded in the genome of an organism into functional biological networks. We have constructed a model for this process in Halobacterium salinarum NRC-1 through the data-driven discovery of regulatory and functional interrelationships among ∼80% of its genes and key abiotic factors in its hypersaline environment. Using relative changes in 72 transcription factors and 9 environmental factors (EFs) this model accurately predicts dynamic transcriptional responses of all these genes in 147 newly collected experiments representing completely novel genetic backgrounds and environments-suggesting a remarkable degree of network completeness. Using this model we have constructed and tested hypotheses critical to this organism's interaction with its changing hypersaline environment. This study supports the claim that the high degree of connectivity within biological and EF networks will enable the construction of similar models for any organism from relatively modest numbers of experiments.

Original languageEnglish (US)
Pages (from-to)1354-1365
Number of pages12
JournalCell
Volume131
Issue number7
DOIs
StatePublished - Dec 28 2007
Externally publishedYes

Fingerprint

Physiology
Cells
Genes
Halobacterium salinarum
Biological Factors
Dynamic response
Transcription Factors
Experiments
Genome

Keywords

  • DNA
  • MICROBIO
  • SYSBIO

ASJC Scopus subject areas

  • Cell Biology
  • Molecular Biology

Cite this

Bonneau, R., Facciotti, M. T., Reiss, D. J., Schmid, A. K., Pan, M., Kaur, A., ... Baliga, N. S. (2007). A Predictive Model for Transcriptional Control of Physiology in a Free Living Cell. Cell, 131(7), 1354-1365. https://doi.org/10.1016/j.cell.2007.10.053

A Predictive Model for Transcriptional Control of Physiology in a Free Living Cell. / Bonneau, Richard; Facciotti, Marc T.; Reiss, David J.; Schmid, Amy K.; Pan, Min; Kaur, Amardeep; Thorsson, Vesteinn; Shannon, Paul; Johnson, Michael; Bare, J. Christopher; Longabaugh, William; Vuthoori, Madhavi; Whitehead, Kenia; Madar, Aviv; Suzuki, Lena; Mori, Tetsuya; Chang, Dong Eun; DiRuggiero, Jocelyne; Johnson, Carl H.; Hood, Leroy; Baliga, Nitin S.

In: Cell, Vol. 131, No. 7, 28.12.2007, p. 1354-1365.

Research output: Contribution to journalArticle

Bonneau, R, Facciotti, MT, Reiss, DJ, Schmid, AK, Pan, M, Kaur, A, Thorsson, V, Shannon, P, Johnson, M, Bare, JC, Longabaugh, W, Vuthoori, M, Whitehead, K, Madar, A, Suzuki, L, Mori, T, Chang, DE, DiRuggiero, J, Johnson, CH, Hood, L & Baliga, NS 2007, 'A Predictive Model for Transcriptional Control of Physiology in a Free Living Cell', Cell, vol. 131, no. 7, pp. 1354-1365. https://doi.org/10.1016/j.cell.2007.10.053
Bonneau R, Facciotti MT, Reiss DJ, Schmid AK, Pan M, Kaur A et al. A Predictive Model for Transcriptional Control of Physiology in a Free Living Cell. Cell. 2007 Dec 28;131(7):1354-1365. https://doi.org/10.1016/j.cell.2007.10.053
Bonneau, Richard ; Facciotti, Marc T. ; Reiss, David J. ; Schmid, Amy K. ; Pan, Min ; Kaur, Amardeep ; Thorsson, Vesteinn ; Shannon, Paul ; Johnson, Michael ; Bare, J. Christopher ; Longabaugh, William ; Vuthoori, Madhavi ; Whitehead, Kenia ; Madar, Aviv ; Suzuki, Lena ; Mori, Tetsuya ; Chang, Dong Eun ; DiRuggiero, Jocelyne ; Johnson, Carl H. ; Hood, Leroy ; Baliga, Nitin S. / A Predictive Model for Transcriptional Control of Physiology in a Free Living Cell. In: Cell. 2007 ; Vol. 131, No. 7. pp. 1354-1365.
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